Abstract: The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.

Abstract: A method of identifying extant proteins, including (a) inputting to a computer processor: (i) a plurality of empirical binding profiles, individual empirical binding profiles including empirical binding outcomes for binding of an extant protein to a plurality of different affinity reagents, (ii) a plurality of candidate outcome profiles, individual candidate outcome profiles including binding outcomes for binding of a candidate protein to the plurality of different affinity reagents, and (iii) a plurality of pseudo outcome profiles, individual pseudo outcome profiles including a rearrangement of a candidate outcome profile; (b) performing a process in the computer processor to identify extant proteins based on the empirical binding profiles of the extant proteins and the plurality of candidate outcome profiles; and (c) performing a process in the computer processor to determine a false discovery statistic for the extant proteins based on the plurality of pseudo outcome profiles.

Abstract: Compositions, systems, and methods are disclosed for preparing and utilizing arrays, such as single-analyte arrays containing a plurality of fiducial elements with random spatial distributions. Arrays may be prepared with pluralities of fiducial elements comprising optically active or passive moieties. Arrays containing random spatial distributions of fiducial elements may be utilized for various array-based processes that require spatial information.

Abstract: A method of identifying an extant protein, including (a) providing inputs including: (i) a binding profile, wherein the binding profile includes a plurality of binding outcomes for binding of the extant protein to a plurality of different affinity reagents, wherein individual binding outcomes of the plurality of binding outcomes include a measure of binding between the extant protein and a different affinity reagent of the plurality of different affinity reagents, (ii) a database including information characterizing or identifying a plurality of candidate proteins, and (iii) a binding model; (b) determining a probability for each of the affinity reagents binding to each of the candidate proteins in the database according to the binding model; and (c) identifying the extant protein as a selected candidate protein having a probability for binding each of the affinity reagents that is most compatible with the binding profile for the extant protein.

Abstract: RFID systems may be configured to use session-dependent replies. When an RFID tag is involved in a certain inventorying session, the tag may respond to inventorying commands with a reply that is at least partly generated based on the session. For example, the tag may generate a reply with a string that has parity based on the session or includes an identifier for the session. The string may be a random number, a tag identifier or item identifier, or any other suitable data sent from the tag.

Abstract: Methods for performing procedures on single analytes at single-analyte resolution are disclosed. The methods utilize an iterative approach to performing a sequence of steps during a single-analyte process. Control of the single-analyte process is achieved by implementing actions during each iteration based upon one or more determined process metrics. Systems are also detailed for implementing the disclosed methods at single-analyte resolution.

Abstract: The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.

Abstract: RFID systems may be configured to use session-dependent replies. When an RFID tag is involved in a certain inventorying session, the tag may respond to inventorying commands with a reply that is at least partly generated based on the session. For example, the tag may generate a reply with a string that has parity based on the session or includes an identifier for the session. The string may be a random number, a tag identifier or item identifier, or any other suitable data sent from the tag.

Abstract: RFID system components, such as readers and tags, communicate where the reader inventories a population of tags. The reader evaluates responses from tags by categorizing them in slots. As tags are inventoried, the number of slots based on a Q-parameter is reduced. The reader reduces the Q-parameter first in a first manner, then in a second manner where the second manner is different from the first manner. The first manner and the second manner may be different algorithms, different subroutines of an algorithm, or the same damping algorithm with different damping parameters.

Abstract: RFID system components, such as readers and tags, communicate where the reader inventories a population of tags. The reader evaluates responses from tags by categorizing them in slots. As tags are inventoried, the number of slots based on a Q-parameter is reduced. The reader determines an interim value for the Q parameter, generates a Q1 value by applying the interim value to a damping function, and uses the Q1 value in another round of interrogation. The reader then determines whether to increase or decrease the interim value depending on the tag replies. The increase or decrease may be an increment or a decrement such as incrementing or decrementing a floating point number of the interim value in a damping function that is arranged to return an integer by rounding the floating point number.

Abstract: An RFID reader inventories a population of tags. The reader evaluates responses from tags by categorizing them in slots. As tags are inventoried, the number of slots based on a Q-parameter is reduced. The reader addresses the tags by communicating a Q1 value for the Q parameter, generates first contents from replies received from the tags, and computes a first merit statistic based on the first contents. Then, the reader repeats the process with a Q2 value. Upon computing the first and the second merit statistics, the reader determines a Q3 value for the Q parameter. If the Q3 value is substantially equal to the Q1 value, the reader continues to receive the second replies without communicating the Q3 value. If the Q3 value is different from the Q2 value, the reader uses the Q3 value for another round of iteration heuristically converging on an optimum Q value.

Abstract: RFID system components, such as readers and tags, communicate where the reader inventories a population of tags. The tags choose randomly one of a plurality of slots in response to each one of the values communicated by the reader and reply according to their chosen slot. The reader may initiate the inventorying by determining a Q-parameter value from a stored value and communicating the Q-parameter value to the tags. The reader may evaluate replies received from the tags in another plurality of tags, determine a second value from evaluating the second replies, and store the second value for future use.

Abstract: An RFID reader inventories a population of tags. The reader evaluates responses from tags by categorizing them in slots. As tags are inventoried, the number of slots based on a Q-parameter is reduced. The reader addresses the tags by communicating a Q1 value for the Q parameter, generates first contents from replies received from the tags, and computes a first merit statistic based on the first contents. Next, the reader determines a Q2 value for the Q parameter, which if used in the same way would meet a preset fairway condition better than the first merit statistic. After determining the Q2 value, the reader addresses a portion of the tags by communicating the Q2 value for the Q parameter.